GNU bug report logs - #25598
R packages are not bit-reproducible

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Message #20 received at 25598 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Guix-devel <guix-devel <at> gnu.org>
Cc: 25598 <at> debbugs.gnu.org
Subject: Re: [PATCH] More reproducibility fixes for R.
Date: Wed, 08 Mar 2017 18:56:34 +0100

Ricardo Wurmus <ricardo.wurmus <at> mdc-berlin.de> writes:

> attached are more reproducibility fixes for R.  Unfortunately, it seems
> that files of type “rdb”, “rdx”, and “rds” are still not reproducible.
> This leaves us with the following files in R that are currently not
> reproducible:

[…]
> /lib/R/library/boot/help/paths.rds
> /lib/R/library/class/help/paths.rds
> /lib/R/library/cluster/help/paths.rds
> /lib/R/library/codetools/help/paths.rds
> /lib/R/library/foreign/help/paths.rds
> /lib/R/library/KernSmooth/help/paths.rds
> /lib/R/library/lattice/help/paths.rds
> /lib/R/library/MASS/help/paths.rds
> /lib/R/library/Matrix/help/paths.rds
> /lib/R/library/mgcv/help/paths.rds
> /lib/R/library/nlme/help/paths.rds
> /lib/R/library/nnet/help/paths.rds
> /lib/R/library/rpart/help/paths.rds
> /lib/R/library/spatial/help/paths.rds
> /lib/R/library/survival/help/paths.rds
[…]
>
> I’ll try to figure out if there’s something we can do to make them
> reproducible (there’s a Debian bug report with relevant information).  I
> had originally assumed that 3.3.2 already included fixes for this.

The paths.rds files contain temporary paths like this:

    /tmp/guix-build-r-3.3.2.drv-0/RtmpCmeE9W/R.INSTALL43fb733deccc/survival/

These paths contain the random strings produced by “mkdtemp”.  This
happens in “src/main/sysutils.c”.

I don’t know if we need these files.  All of them are part of the
recommended packages.  I don’t know if these are also built by Debian.

I patched the package in a previous commit to override the built
timestamp, and it does seem to have an effect on the DESCRIPTION file,
but it does not affect the .rd* files.  More investigation required.

--
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net

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